Merge branch 'release/0.1.22'

.github/workflows/osf_data_to_release_assets.yml

@@ -0,0 +1,78 @@
+# https://osf.io/tvmf8 files to github release assets
+name: OSF data to release assets
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  build:
+    name: Upload assets to release
+    runs-on: ubuntu-latest
+    steps:
+
+    - name: wget
+      uses: wei/wget@v1
+      with:
+        args: -O fastq.tar.gz https://osf.io/9mvzw/download
+    - name: wget fastq.tar.gz to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: fastq.tar.gz
+        asset_name: fastq.tar.gz
+        tag: ${{ github.ref }}
+        overwrite: true
+
+    - name: wget
+      uses: wei/wget@v1
+      with:
+        args: -O sorted.tar.gz https://osf.io/dhk5g/download
+    - name: wget sorted.tar.gz to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: sorted.tar.gz
+        asset_name: sorted.tar.gz
+        tag: ${{ github.ref }}
+        overwrite: true
+
+    - name: wget
+      uses: wei/wget@v1
+      with:
+        args: -O taxonomy.tsv.gz https://osf.io/uzk87/download
+    - name: wget taxonomy.tsv.gz to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: taxonomy.tsv.gz
+        asset_name: taxonomy.tsv.gz
+        tag: ${{ github.ref }}
+        overwrite: true
+
+    - name: wget
+      uses: wei/wget@v1
+      with:
+        args: -O coi_blast_db.tar.gz https://osf.io/45zfd/download
+    - name: wget coi_blast_db.tar.gz to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: coi_blast_db.tar.gz
+        asset_name: coi_blast_db.tar.gz
+        tag: ${{ github.ref }}
+        overwrite: true
+
+    - name: wget
+      uses: wei/wget@v1
+      with:
+        args: -O coi_blast_db_20200420.tar.gz https://osf.io/kw9ms/download
+    - name: wget coi_blast_db_20200420.tar.gz to release
+      uses: svenstaro/upload-release-action@v2
+      with:
+        repo_token: ${{ secrets.GITHUB_TOKEN }}
+        file: coi_blast_db_20200420.tar.gz
+        asset_name: coi_blast_db_20200420.tar.gz
+        tag: ${{ github.ref }}
+        overwrite: true

.github/workflows/run-tests.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.6, 3.7, 3.8, 3.9, "3.10"]
 
     steps:
     - uses: actions/checkout@v2
@@ -24,19 +24,20 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Setup environment
       run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          conda create -q -n vtam
-          source activate vtam
-          conda env update -f environment.yml
+          # export PATH="/usr/share/miniconda/bin:$PATH"
+          $CONDA/bin/conda create -y -q --name vtam python=${{ matrix.python-version }}
+          # source activate vtam
+          $CONDA/bin/conda env update -f environment.yml --name vtam
     - name: Run tests
       env:
         CI: true
       run: |
         # activate conda env
-        export PATH="/usr/share/miniconda/bin:$PATH"
-        source activate vtam
-        vsearch --version
-        cutadapt --version
-        blastn -version
-        python -m unittest discover -v -f
+        export PATH="$CONDA/envs/vtam/bin:$PATH"
+        #source activate base
+        $CONDA/envs/vtam/bin/vsearch --version
+        $CONDA/envs/vtam/bin/cutadapt --version
+        $CONDA/envs/vtam/bin/blastn -version
+        $CONDA/envs/vtam/bin/python --version
+        $CONDA/envs/vtam/bin/python -m unittest discover -v -f
 

.travis.yml

@@ -4,6 +4,7 @@ python:
   - "3.6"
   - "3.7"
   - "3.8"
+  - "3.9"
 notifications:
   email: false
 before_install:

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2018-2020 Aitor Gonzalez, Emese Meglecz
+Copyright (c) 2018-2022 Aitor Gonzalez, Emese Meglecz
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -14,9 +14,6 @@ VTAM - Validation and Taxonomic Assignation of Metabarcoding Data
 .. image:: https://github.com/aitgon/vtam/workflows/CI/badge.svg
     :target: https://github.com/aitgon/vtam/actions?query=branch%3Amaster+workflow%3ACI
 
-.. image:: https://travis-ci.org/aitgon/vtam.svg?branch=master
-    :target: https://travis-ci.org/aitgon/vtam
-
 .. image:: https://codecov.io/gh/aitgon/vtam/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/aitgon/vtam
 
@@ -31,11 +28,17 @@ Commands for a quick installation:
 
 .. code-block:: bash
 
-    conda create --name vtam python=3.7 -y
-    python3 -m pip install --upgrade cutadapt
-    conda install -c bioconda blast
-    conda install -c bioconda vsearch
-    python3 -m pip install --upgrade vtam
+    conda create --name vtam python=3.9 -y
+    conda activate vtam
+
+Then install dependencies
+
+.. code-block:: bash
+
+    python3 -m pip install cutadapt
+    conda install -c bioconda blast -y
+    conda install -c bioconda vsearch -y
+    python3 -m pip install vtam
 
 Commands for a quick working example:
 

RELEASE.rst

@@ -1,3 +1,7 @@
+**Changes In Version 0.1.22 (Jan 31, 2022)**
+
+- Updated and tested with python 3.9 and 3.10
+
 **Changes In Version 0.1.21 (Dec 11, 2020)**
 
 - ENH added '--countreads' option to 'vtam pool'

doc/content/installation.rst

@@ -39,6 +39,22 @@ You can also verify the BLAST (>=  v2.2.26), CutAdapt (>= 2.10) and VSEARCH (>=
     cutadapt --version
     vsearch --version
 
+Singularity
+-------------------------------------------------
+
+We provide a singularity container in the VTAM github: https://github.com/aitgon/vtam .
+First you build the image with this command as root:
+
+.. code-block:: bash
+
+    sudo singularity build vtam.sif vtam.singularity
+
+Then you can use VTAM directly from the singularity image:
+
+.. code-block:: bash
+
+    singularity run --app vtam vtam.sif --help
+    singularity run --app vtam vtam.sif merge --help
 
 Windows
 -------------------------------------------------

environment-dev.yml

@@ -2,10 +2,9 @@ channels:
   - defaults
   - bioconda
 dependencies:
-  - python=3.7
   - blast
   - vsearch
   - pip
   - pip:
-    - -r file:requirements-dev.txt
+    - -r requirements-dev.txt
 

environment.yml

@@ -2,10 +2,9 @@ channels:
   - defaults
   - bioconda
 dependencies:
-  - python=3.7
   - blast
   - vsearch
   - pip
   - pip:
-    - -r file:requirements.txt
+    - -r requirements.txt
 

requirements.txt

@@ -1,5 +1,5 @@
 biopython
-cutadapt==2.10
+cutadapt
 jinja2
 pandas
 pyyaml

setup.cfg

@@ -2,7 +2,7 @@
 description-file = README.rst
 author = Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz
 email = aitor.gonzalez@univ-amu.fr
-copyright = Copyright (c) 2018-2020: Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz
+copyright = Copyright (c) 2018-2022: Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz
 license = MIT
 
 [easy_install]

setup.py

@@ -1,7 +1,7 @@
 # -*- coding: UTF-8 -*-
 
 __author__ = "Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz"
-__copyright__ = "Copyright 2018-2020, Aitor Gonzalez, Emese Meglecz"
+__copyright__ = "Copyright 2018-2022, Aitor Gonzalez, Emese Meglecz"
 __email__ = "aitor.gonzalez@univ-amu.fr, emese.meglecz@univ-amu.fr"
 __license__ = "MIT"
 
@@ -33,33 +33,6 @@
 with open(os.path.join(here, 'README.rst'), encoding='utf-8') as fin:
     long_description = fin.read()
 
-CLASSIFIERS = """\
-Development Status :: 4 - Beta
-Environment :: Console
-Intended Audience :: Science/Research
-License :: OSI Approved :: MIT License
-Programming Language :: Python
-Programming Language :: Python :: 3
-Programming Language :: Python :: 3.7
-Programming Language :: Python :: 3 :: Only
-Topic :: Scientific/Engineering :: Bio-Informatics
-Operating System :: POSIX :: Linux
-Operating System :: Microsoft :: Windows :: Windows 10
-"""
-
-
-# Create list of package data files
-def data_files_to_list(directory):
-    paths = []
-    for (path, directories, filenames) in os.walk(directory):
-        for filename in filenames:
-            paths.append(os.path.join('..', path, filename))
-    return paths
-
-
-data_file_list = data_files_to_list('vtam/data')
-data_example_file_list = data_files_to_list('vtam/data/example')
-
 def read(rel_path):
     here = os.path.abspath(os.path.dirname(__file__))
     with codecs.open(os.path.join(here, rel_path), 'r') as fp:
@@ -73,21 +46,6 @@ def get_version(rel_path):
     else:
         raise RuntimeError("Unable to find version string.")
 
-if sys.version_info < (3, 7):
-    print("At least Python 3.7 is required.\n", file=sys.stderr)
-    exit(1)
-
-try:
-    from setuptools import setup, find_packages
-except ImportError:
-    print("Please install setuptools before installing VTAM.",
-          file=sys.stderr)
-    exit(1)
-
-here = os.path.abspath(os.path.dirname(__file__))
-with open(os.path.join(here, 'README.rst'), encoding='utf-8') as fin:
-    long_description = fin.read()
-
 CLASSIFIERS = """\
 Development Status :: 4 - Beta
 Environment :: Console
@@ -98,6 +56,8 @@ def get_version(rel_path):
 Programming Language :: Python :: 3.6
 Programming Language :: Python :: 3.7
 Programming Language :: Python :: 3.8
+Programming Language :: Python :: 3.9
+Programming Language :: Python :: 3.10
 Programming Language :: Python :: 3 :: Only
 Topic :: Scientific/Engineering :: Bio-Informatics
 Topic :: Software Development
@@ -120,9 +80,9 @@ def data_files_to_list(directory):
     name='vtam',
     version=get_version("vtam/__init__.py"),
     description="VTAM - Validation and Taxonomic Assignation of Metabarcoding Data "
-                "is a metabarcoding pipeline. The analyses start from high throughput "
+                "is a metabarcoding pipeline. The analysis starts from high throughput "
                 "sequencing (HTS) data of amplicons of one or several metabarcoding "
-                "markers and produce an amplicon sequence variant (ASV) "
+                "markers and produces an amplicon sequence variant (ASV) "
                 "table of validated variants assigned to taxonomic groups.",
     author=author,
     author_email=email,
@@ -133,7 +93,7 @@ def data_files_to_list(directory):
     packages=find_packages(),
     package_dir={'vtam': 'vtam'},
     package_data={'vtam': data_file_list},
-    install_requires=['biopython', 'cutadapt', 'jinja2', 'pandas', 'progressbar', 'pyyaml', 'sqlalchemy', 'snakemake', 'termcolor', 'wopmars'],
+    install_requires=['biopython', 'cutadapt', 'jinja2', 'pandas', 'progressbar', 'pyyaml', 'sqlalchemy', 'snakemake', 'termcolor', 'tqdm', 'wopmars'],
     entry_points={
         'console_scripts': ['vtam=vtam:main']
     },